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bioinform / somaticseq

An ensemble approach to accurately detect somatic mutations using SomaticSeq
http://bioinform.github.io/somaticseq/
BSD 2-Clause "Simplified" License
189 stars 53 forks source link

Result of TNscope caller #111

Closed yoda0612 closed 2 years ago

yoda0612 commented 2 years ago

Hi, I am working with your somaticseq. I'd like to ask if I want to use the result of TNscope caller as the one of the inputs, how should I do? Thank you.

litaifang commented 2 years ago

You can see all the available parameters before paired by command somaticseq_parallel.py -h, and all the available parameters after paired by command somaticseq_parallel.py paired -h. For TNscope, the argument would be --tnscope-vcf tnscope_calls.vcf.gz.

yoda0612 commented 2 years ago

Thank you for your reply. Yes, as you mentioned the --tnscope-vcf seems worked only in "paired" mode. Is it possible to use --tnscope-vcf in "single" mode?

litaifang commented 2 years ago

I did not explicitly incorporate TNscope into the single mode. But in the latest version, there is a way to use the result of any additional caller, i.e., --arbitrary-snvs and --arbitrary-indels. First, you'll need to separate the snvs and indels by doing splitVcf.py -infile TNscope.vcf.gz -snv tnscope_snvs.vcf -indel tnscope_indels.vcf.

yoda0612 commented 2 years ago

Thanks a lot